General information for g16136.t12
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cofilin/actin-depolymerizing factor-like protein.
Parent gene
- The parent gene g16136 is located on chr_4: 8338443..8342935 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_4 | g16136 | g16136.t12 | isoform | g16136.t12 | 8338182 | 8342707 |
| chr_4 | g16136 | g16136.t12 | exon | g16136.t12.exon1 | 8338182 | 8338397 |
| chr_4 | g16136 | g16136.t12 | TTS | g16136.t12 | 8338183 | 8338183 |
| chr_4 | g16136 | g16136.t12 | cds | g16136.t12.CDS1 | 8338336 | 8338397 |
| chr_4 | g16136 | g16136.t12 | exon | g16136.t12.exon2 | 8338472 | 8338589 |
| chr_4 | g16136 | g16136.t12 | cds | g16136.t12.CDS2 | 8338472 | 8338589 |
| chr_4 | g16136 | g16136.t12 | exon | g16136.t12.exon3 | 8338651 | 8338947 |
| chr_4 | g16136 | g16136.t12 | cds | g16136.t12.CDS3 | 8338651 | 8338947 |
| chr_4 | g16136 | g16136.t12 | exon | g16136.t12.exon4 | 8342705 | 8342707 |
| chr_4 | g16136 | g16136.t12 | cds | g16136.t12.CDS4 | 8342705 | 8342707 |
| chr_4 | g16136 | g16136.t12 | TSS | g16136.t12 | 8342954 | 8342954 |
Sequences
>g16136.t12 Gene=g16136 Length=634
ATGGCTTCCGGAGTAACTGTCTCAGATGTTTGTAAGACAACATATGAAGAAATTAAGAAG
GACAAAAAACATCGCTATGTAATTTTTTACATTCGTGATGAGAAGCAAATTGATGTGGAA
GTGATTGGTGAACGTAATGCAGAATATGATTCGTTCCTTGAAGATATTCAAAAAGGCGGT
CCAGGTGAATGCCGATATGGACTCTTTGATTTTGAGTATATGCATCAATGTCAAGGCACC
TCTGAGAGTTCCAAGAAGCAAAAATTATTTTTAATGTCCTGGTGTCCAGATACTGCTAAA
GTCAAGAAGAAGATGTTGTACTCAAGCTCATTTGATGCATTGAAAAAGTCACTTGTAGGT
GTGCAAAAATACATTCAAGCTACAGACTTATCAGAGGCCTCACGTGAAGCTGTTGAAGTT
TTGAATTATTATTATTATTATTTTGCAACAATTACATCAAATTTATCTATTCATTTATAA
AATGTGTCAACAAATTAATTTTCTCTCCCCATTTTATTTGTCTCATTTTTTAAATAAAAA
AAATAATTAAAGTAATTAATTATTGATTAAAATAAACTCAAAAACTGAAAAAGAACATTT
AAATAAAAATGATTTTTTAAGTTTTATTAGCTGA
>g16136.t12 Gene=g16136 Length=159
MASGVTVSDVCKTTYEEIKKDKKHRYVIFYIRDEKQIDVEVIGERNAEYDSFLEDIQKGG
PGECRYGLFDFEYMHQCQGTSESSKKQKLFLMSWCPDTAKVKKKMLYSSSFDALKKSLVG
VQKYIQATDLSEASREAVEVLNYYYYYFATITSNLSIHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g16136.t12 | CDD | cd11286 | ADF_cofilin_like | 3 | 139 | 0.000 |
| 6 | g16136.t12 | Gene3D | G3DSA:3.40.20.10 | Severin | 1 | 142 | 0.000 |
| 2 | g16136.t12 | PANTHER | PTHR11913:SF12 | COFILIN/ACTIN-DEPOLYMERIZING FACTOR HOMOLOG-RELATED | 2 | 138 | 0.000 |
| 3 | g16136.t12 | PANTHER | PTHR11913 | COFILIN-RELATED | 2 | 138 | 0.000 |
| 1 | g16136.t12 | Pfam | PF00241 | Cofilin/tropomyosin-type actin-binding protein | 11 | 138 | 0.000 |
| 7 | g16136.t12 | ProSiteProfiles | PS51263 | ADF-H domain profile. | 4 | 143 | 30.046 |
| 5 | g16136.t12 | SMART | SM00102 | adf_2 | 9 | 143 | 0.000 |
| 4 | g16136.t12 | SUPERFAMILY | SSF55753 | Actin depolymerizing proteins | 1 | 138 | 0.000 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003779 | actin binding | MF |
| GO:0015629 | actin cytoskeleton | CC |
| GO:0030042 | actin filament depolymerization | BP |
KEGG
Orthology
- This transcript has been annotated with K05765 (cofilin)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed